Approximating algorithm for RNA structure prediction including pseudoknots.

RNA structure and tertiary structure could be represented by a set of nested arcs and a set of crossing arcs. Based on the relative stability of the stems in RNA molecules, an approximating algorithm is presented to predict RNA pseudoknotted structure, the algorithm takes O(n3) time and O(n) space, the algorithm outperforms other known algorithms in predicting accuracy. This algorithm not only reduces the time complexity to O(n3), but also widens the maximum length of the sequence. The preliminary experimental test on the RNA subsequences in PseudoBase confirm that the algorithm has good sensitivity and specificity, and are among the most reasonable in the literature. © 2011 IEEE.